X-Ray Tomography on Intestine Samples

Abstract

Enteric neuropathy describes a disease of the bowel caused by anomalies in the enteric nervous system. Patients suffering from this disease have symptoms including nausea, vomiting, diarrhea and pain. As enteric neuropathy is not well understood yet, its diagnosis is a non-trivial task.

Research on the enteric nervous system is needed in order to gain a better understanding of this disease, making a correct diagnosis and targeted treatment possible. Thus, this thesis presents the investigation of nervous cells in the bowel and different setups that can be used for this purpose. More specifically, this involves the recording of high-resolution 3D images, with the ultimate aim to segment the ganglia, that are made up of neurons, in the intestinal samples to determine their volumes and compare the ganglia volumes of samples from healthy with those of diseased patients. In order to do this, X-ray tomography based on absorption and phase contrast was performed.

This master thesis presents the comparison of two experimental setups, namely a lab based micro-CT in Lund, Sweden and the TOMCAT beamline at the Paul-Scherrer-Institut in Villigen, Switzerland, that were used to carry out these studies. It was concluded that the setups could not be compared in terms of contrast-to-noise ratio, as their determination was not successful. Regarding the resolution, it was found that the micro-CT setup is appropriate to perform overview scans of the sample, but its overall resolution is not high enough for the successful segmentation of the ganglia. In contrast,
the TOMCAT setup delivered a resolution sufficient for the ganglias’ segmentation. The visibility of the ganglia could be significantly improved by applying phase retrieval, using the Paganin algorithm, to the datasets before their reconstruction due to this procedure enhancing the contrast. A reconstruction of the TOMCAT data with a self-developed script was conducted and compared to the reconstruction that was done directly at the beamline. It was found that the self-developed reconstruction was successful overall, but not optimal when it came to applying the Paganin algorithm, leading to an ambiguous separation between tissue and background. Furthermore, the optimal δ/β ratio for the phase retrieval reconstruction at the micro-CT setup was confirmed to be 217.6. After these preparations to find the optimal conditions for the segmentation of ganglia, the volumes of the ganglia, remaining biological tissue and background were determined to be 0.011 mm3, 0.44 mm3 and 0.067 mm3 in a 0.5 mm3 volume of one sample. The segmentation and subsequent determination of the volumes of further ganglia will pave the way for gaining a deeper knowledge of enteric neuropathy.

Popular Abstract

Unfortunately, many people suffer from chronic intestinal diseases that restrict them in their daily lives. Symptoms of these diseases can include diarrhea, nausea and vomiting. In many cases it is difficult to help them as the circumstances leading to the symptoms are not always clear. The persons affected can only receive helpful treatment if the disease is generally well understood and correctly diagnosed.

One type of disease that can cause the aforementioned symptoms, but is not yet well understood, involves the alteration of specific nerve cells in the bowel. One way to better understand this condition is to study the morphological changes that occur in the affected cells. For this purpose, it is necessary to take images of the cells.

Until now, the cells have been pictured by taking samples from patients via biopsy or surgery and then examining them with microscopes. The problem is that it is difficult to see such small structures in detail with normal microscopes (that means the information is incomplete) and that only very thin layers of the samples can be examined because of the low penetration power of visible light. The need for thin layers means that the sample has to be sectioned and can therefore be damaged, motivating the recording of 3D images.

In order to investigate the whole sample volume, i.e. record 3D images, light in form of X-rays can be used. Imaging is based on interaction between light and matter, more specifically between light and electrons in the matter. As X-rays have an energy more than one thousand times higher than that of visible light, they penetrate deeper into the atoms and interact with the core electrons, which only make up a small fraction of the atom’s electrons. Due to this small interaction, matter is more transparent to X-rays. Having high-energy light is also accompanied by a short wavelength. The shorter the wavelength, the higher the resolution that can be achieved. Consequently, X-rays also help with resolving small features such as nerve cells and can be thought of as a super microscope.

If one does not only consider the amount of X-rays that pass through the sample, but also how they are deflected, the contrast can be increased. This works like a very powerful zoom function on a camera and makes it possible to see the nerve cells with high resolution and many details without destroying the sample.

The aim of this thesis was to record 3D high-resolution images of nerve cells by using X-rays as a “super microscope” to get started analyzing morphological alterations of these cells. This will help us learn more about chronic diseases that are caused by these changes, something that will be necessary to be able to carry out targeted treatment.

• author: Rogalinski, Julia
• supervisor: Pablo Villanueva Perez; Martin Bech
• organization: Synchrotron Radiation Research; Department of Physics
• course: FYSM30 20222
• year: 2023
• type: H2 - Master's Degree (Two Years)
• subject: Physics and Astronomy
• language: English
• id: 9108817
• date added to LUP: 2023-01-27 11:20:59
• date last changed: 2023-01-27 11:20:59